rs10491749

Variant names:

• chr9-12364913-C-T
• rs10491749

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0975 in 151,950 control chromosomes in the GnomAD database, including 940 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.098 (940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0975 AC: 14801 AN: 151834 Hom.: 939 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0912

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0578

Gnomad OTH AF: 0.0952

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0975 AC: 14816 AN: 151950 Hom.: 940 Cov.: 32 AF XY: 0.101 AC XY: 7503 AN XY: 74258

African (AFR) AF: 0.154 AC: 6398 AN: 41462

American (AMR) AF: 0.0547 AC: 834 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0912 AC: 316 AN: 3466

East Asian (EAS) AF: 0.243 AC: 1248 AN: 5144

South Asian (SAS) AF: 0.191 AC: 921 AN: 4812

European-Finnish (FIN) AF: 0.0877 AC: 926 AN: 10564

Middle Eastern (MID) AF: 0.0690 AC: 20 AN: 290

European-Non Finnish (NFE) AF: 0.0578 AC: 3928 AN: 67954

Other (OTH) AF: 0.0966 AC: 204 AN: 2112

Alfa AF: 0.0753 Hom.: 446

Bravo AF: 0.0976

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.39
PhyloP100		-0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10491749; hg19: chr9-12364913;